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Chore/update deps #638

Merged
merged 22 commits into from
Oct 16, 2024
Merged

Chore/update deps #638

merged 22 commits into from
Oct 16, 2024

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bartcharbon
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@bartcharbon bartcharbon commented Oct 7, 2024 •
edited by dennishendriksen
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cram/complex                             | PASSED | 271950=completed output/cram/complex/.nxf.log                                  
cram/multiproject                        | PASSED | 271951=completed output/cram/multiproject/.nxf.log
cram/nanopore_duo                        | PASSED | 271952=completed output/cram/nanopore_duo/.nxf.log                              
cram/nanopore                            | PASSED | 271953=completed output/cram/nanopore/.nxf.log
cram/single                              | PASSED | 271954=completed output/cram/single/.nxf.log                                    
cram/trio                                | PASSED | 271955=completed output/cram/trio/.nxf.log
fastq/nanopore_adaptive_sampling         | PASSED | 271956=completed output/fastq/nanopore_adaptive_sampling/.nxf.log               fastq/nanopore                           | PASSED | 271957=completed output/fastq/nanopore/.nxf.log
fastq/pacbio_hifi                        | PASSED | 271958=completed output/fastq/pacbio_hifi/.nxf.log                              
gvcf/liftover                            | PASSED | 271959=completed output/gvcf/liftover/.nxf.log
gvcf/multiproject                        | PASSED | 271960=completed output/gvcf/multiproject/.nxf.log                              
gvcf/trio                                | PASSED | 271961=completed output/gvcf/trio/.nxf.log
vcf/aip                                  | PASSED | 271962=completed output/vcf/aip/.nxf.log                                        
vcf/chd7                                 | PASSED | 271963=completed output/vcf/chd7/.nxf.log
vcf/corner_cases                         | PASSED | 271964=completed output/vcf/corner_cases/.nxf.log                               
vcf/deb_register                         | PASSED | 271965=completed output/vcf/deb_register/.nxf.log
vcf/empty_input                          | PASSED | 271966=completed output/vcf/empty_input/.nxf.log                               
vcf/empty_output_filter_samples          | PASSED | 271967=completed output/vcf/empty_output_filter_samples/.nxf.log
vcf/empty_output_filter                  | PASSED | 271968=completed output/vcf/empty_output_filter/.nxf.log
vcf/filter_samples                       | PASSED | 271969=completed output/vcf/filter_samples/.nxf.log
vcf/liftover                             | PASSED | 271970=completed output/vcf/liftover/.nxf.log                                   
vcf/multiproject_classify                | PASSED | 271971=completed output/vcf/multiproject_classify/.nxf.log
vcf/mvid                                 | PASSED | 271972=completed output/vcf/mvid/.nxf.log
vcf/str                                  | PASSED | 271973=completed output/vcf/str/.nxf.log
vcf/trio                                 | PASSED | 271974=completed output/vcf/trio/.nxf.log
vcf/vkgl_lb                              | PASSED | 271975=completed output/vcf/vkgl_lb/.nxf.log
vcf/vkgl_lp                              | PASSED | 271976=completed output/vcf/vkgl_lp/.nxf.log
vcf/vkgl_vus                             | PASSED | 271977=completed output/vcf/vkgl_vus/.nxf.log

@bartcharbon bartcharbon marked this pull request as ready for review October 10, 2024 05:44
dennishendriksen
dennishendriksen requested changes Oct 14, 2024
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utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated
%post
# install
apk update
apk add gcc zlib zlib-dev libc-dev gcompat libstdc++
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(some of) these libraries are only needed to build native images? if yes, they can be removed

utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated Show resolved Hide resolved
utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated
%environment
JAVA_HOME=/usr/lib/jvm/graalvm-community-openjdk-21.0.2+13.1
#workaround to solve "Unable to load jimage library"
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$JAVA_HOME/lib/server
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is this workaround required when the image is not used to build native images?

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Yes, our images did not work without it

utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated
wget "https://github.com/graalvm/graalvm-ce-builds/releases/download/jdk-21.0.2/graalvm-community-jdk-21.0.2_linux-x64_bin.tar.gz"; \
tar -xzf graalvm-community-jdk-21.0.2_linux-x64_bin.tar.gz -C /usr/lib/jvm; \
rm -f graalvm-ce-21.0.2-linux-amd64.tar.gz

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add cleanup

# cleanup
apk del .build-dependencies

utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated Show resolved Hide resolved
utils/apptainer/def/build/graalvm-ce-21.0.2.def Outdated
# install
apk update
apk add gcc zlib zlib-dev libc-dev gcompat libstdc++
apk add --virtual=.build-dependencies ca-certificates wget
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should we keep ca-certificates? see e.g. https://github.com/findepi/graalvm-docker/blob/master/Dockerfile

@dennishendriksen dennishendriksen merged commit 7aabbcb into main Oct 16, 2024
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@dennishendriksen dennishendriksen deleted the chore/update-deps branch October 16, 2024 09:13
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@bartcharbon @dennishendriksen